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WO2024010812A3 - Methods and systems for determining copy number variant genotypes - Google Patents

Methods and systems for determining copy number variant genotypes Download PDF

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Publication number
WO2024010812A3
WO2024010812A3 PCT/US2023/026935 US2023026935W WO2024010812A3 WO 2024010812 A3 WO2024010812 A3 WO 2024010812A3 US 2023026935 W US2023026935 W US 2023026935W WO 2024010812 A3 WO2024010812 A3 WO 2024010812A3
Authority
WO
WIPO (PCT)
Prior art keywords
systems
methods
copy number
number variant
hba1
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/US2023/026935
Other languages
French (fr)
Other versions
WO2024010812A2 (en
Inventor
Vitor Ferreira ONUCHIC
Xiao Chen
Shunhua HAN
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Illumina Inc
Illumina Software Inc
Original Assignee
Illumina Inc
Illumina Software Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Illumina Inc, Illumina Software Inc filed Critical Illumina Inc
Priority to CA3260289A priority Critical patent/CA3260289A1/en
Priority to JP2024575797A priority patent/JP2025524474A/en
Priority to US18/866,918 priority patent/US20250246265A1/en
Priority to EP23748377.1A priority patent/EP4552124A2/en
Priority to KR1020247042444A priority patent/KR20250036077A/en
Publication of WO2024010812A2 publication Critical patent/WO2024010812A2/en
Publication of WO2024010812A3 publication Critical patent/WO2024010812A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/10—Ploidy or copy number detection
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

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  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Data Mining & Analysis (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Pathology (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Software Systems (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Bioethics (AREA)
  • Artificial Intelligence (AREA)
  • Evolutionary Computation (AREA)
  • Public Health (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

Disclosed herein are systems, devices, and methods for identifying recombinant variants (such as deletion or duplication variants) of genes such as HBA1 gene and HBA2 gene, the copy numbers of HBA1 and/or HBA2, and a copy number variant genotype. Also disclosed herein are systems, devices, and methods for detecting one or more single-nucleotide variants or indels in a HBA1/2 region in a nucleic acid sample.
PCT/US2023/026935 2022-07-07 2023-07-05 Methods and systems for determining copy number variant genotypes Ceased WO2024010812A2 (en)

Priority Applications (5)

Application Number Priority Date Filing Date Title
CA3260289A CA3260289A1 (en) 2022-07-07 2023-07-05 Methods and systems for determining copy number variant genotypes
JP2024575797A JP2025524474A (en) 2022-07-07 2023-07-05 Methods and systems for determining copy number variation genotypes
US18/866,918 US20250246265A1 (en) 2022-07-07 2023-07-05 Methods and systems for determining copy number variant genotypes
EP23748377.1A EP4552124A2 (en) 2022-07-07 2023-07-05 Methods and systems for determining copy number variant genotypes
KR1020247042444A KR20250036077A (en) 2022-07-07 2023-07-05 Method and system for determining copy number variant genotype

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202263367888P 2022-07-07 2022-07-07
US63/367,888 2022-07-07

Publications (2)

Publication Number Publication Date
WO2024010812A2 WO2024010812A2 (en) 2024-01-11
WO2024010812A3 true WO2024010812A3 (en) 2024-02-15

Family

ID=87517235

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2023/026935 Ceased WO2024010812A2 (en) 2022-07-07 2023-07-05 Methods and systems for determining copy number variant genotypes

Country Status (6)

Country Link
US (1) US20250246265A1 (en)
EP (1) EP4552124A2 (en)
JP (1) JP2025524474A (en)
KR (1) KR20250036077A (en)
CA (1) CA3260289A1 (en)
WO (1) WO2024010812A2 (en)

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2025217057A1 (en) * 2024-04-08 2025-10-16 Illumina, Inc. Variant detection using improved sequence data alignments

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014023076A1 (en) * 2012-08-10 2014-02-13 深圳华大基因科技有限公司 Thalassemia typing method and use thereof
CN108875311A (en) * 2018-06-22 2018-11-23 安徽医科大学第附属医院 Copy number mutation detection method based on high-flux sequence and gauss hybrid models
WO2020249102A1 (en) * 2019-06-13 2020-12-17 北京贝瑞和康生物技术有限公司 Kit and method for detecting both hba1/2 and hbb gene mutations

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5432272A (en) 1990-10-09 1995-07-11 Benner; Steven A. Method for incorporating into a DNA or RNA oligonucleotide using nucleotides bearing heterocyclic bases
CA2122365C (en) 1991-11-26 2010-05-11 Brian Froehler Enhanced triple-helix and double-helix formation with oligomers containing modified pyrimidines
DK0691980T3 (en) 1993-03-30 1997-12-29 Sanofi Sa 7-deazapurine-modifying oligonucleotides
EP0695306A1 (en) 1993-04-19 1996-02-07 Gilead Sciences, Inc. Enhanced triple-helix and double-helix formation with oligomers containing modified purines
US6150510A (en) 1995-11-06 2000-11-21 Aventis Pharma Deutschland Gmbh Modified oligonucleotides, their preparation and their use

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2014023076A1 (en) * 2012-08-10 2014-02-13 深圳华大基因科技有限公司 Thalassemia typing method and use thereof
CN108875311A (en) * 2018-06-22 2018-11-23 安徽医科大学第附属医院 Copy number mutation detection method based on high-flux sequence and gauss hybrid models
WO2020249102A1 (en) * 2019-06-13 2020-12-17 北京贝瑞和康生物技术有限公司 Kit and method for detecting both hba1/2 and hbb gene mutations

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
"Inherited Hemoglobin Disorders", 11 November 2015, INTECHOPEN, tntechopen, ISBN: 978-953-51-7261-1, article EL-KAMAH GHADA Y. ET AL: "Thalassemia - From Genotype to Phenotype | IntechOpen", pages: 1 - 23, XP093090781, DOI: 10.5772/59742 *
WAYE J S ET AL: "Diagnostic testing for [alpha]-globin gene disorders in a heterogeneous North American population", INTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY, WILEY-BLACKWELL PUBLISHING LTD, GB; US, vol. 35, no. 3, 17 April 2013 (2013-04-17), pages 306 - 313, XP072383431, ISSN: 1751-5521, DOI: 10.1111/IJLH.12066 *
YANG JIEXIA ET AL: "Noninvasive prenatal detection of hemoglobin Bart hydrops fetalis via maternal plasma dispensed with parental haplotyping using the semiconductor sequencing platform", AMERICAN JOURNAL OF OBSTETRICS & GYNECOLOGY, MOSBY, ST LOUIS, MO, US, vol. 222, no. 2, 5 August 2019 (2019-08-05), XP086010392, ISSN: 0002-9378, [retrieved on 20190805], DOI: 10.1016/J.AJOG.2019.07.044 *

Also Published As

Publication number Publication date
EP4552124A2 (en) 2025-05-14
JP2025524474A (en) 2025-07-30
KR20250036077A (en) 2025-03-13
CA3260289A1 (en) 2024-01-11
WO2024010812A2 (en) 2024-01-11
US20250246265A1 (en) 2025-07-31

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